Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data

Intergeneric hybrid origin of the invasive tetraploid Cirsium vulgare

The invasive tetraploid Cirsium vulgare hybridizes with both Cirsium and Lophiolepis. Its conflicted position in molecular phylogenies, and its peculiar combination of morphological, anatomical, and genomic features that are alternatively shared with representatives of Cirsium or Lophiolepis, strongly suggest its intergeneric hybrid origin. Genetic relationships of C. vulgare (8 samples) with genus Lophiolepis (11 species) and other representatives of genus Cirsium (12 species) were evaluated using restriction site-associated DNA sequencing (RADseq) and examined using analytical and imaging approaches, such as NeighborNet, Heatmap, and STRUCTURE, to identify nuclear genomes admixture. Estimation of the intensity of spontaneous hybridization within and between Cirsium and Lophiolepis was based on herbarium revisions and published data for all reported hybrids pertinent to taxa currently included in Cirsium or Lophiolepis. The genome of any examined Cirsium species is more similar to C. vulgare than to any Lophiolepis species, and vice versa. The nuclear genome of the tetraploid C. vulgare is composed of two equivalent parts, each attributable either to Lophiolepis or to Cirsium; the organellar RADseq data clustered C. vulgare with the genus Cirsium. Spontaneous hybridization between Cirsium and Lophiolepis is significantly less intensive than within these genera. Our analyses provide compelling evidence that the invasive species C. vulgare has an allotetraploid intergeneric origin, with the maternal parent from Cirsium and the paternal from Lophiolepis. For the purpose of delimiting monophyletic genera, we propose keeping Lophiolepis separate from Cirsium and segregating C. vulgare into the hybridogenous genus Ascalea.

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

Phylogenomic analysis reveals the evolutionary history of Paleartic needle-leaved junipers

Needle-leaved junipers (Juniperus sect. Juniperus, Cupressaceae) are coniferous trees and shrubs with red or blue fleshy cones. They are distributed across Asia, Macaronesia and the Mediterranean Basin, with one species (J. communis) having a circumboreal distribution. Here we aim to resolve the phylogeny of this clade to infer its intricate evolutionary history. To do so, we built a comprehensive, time-calibrated phylogeny using genotyping-by-sequencing (GBS) and combine it with species occurrence using phylogeographic tools. Our results provide solid phylogenetic resolution to propose a new taxonomic classification and a biogeographical history of the section. Specifically, we confirm the monophyly of two groups within J. sect. Juniperus: the Asian (blue-cone) species including the circumboreal J. communis, and the Mediterranean-Macaronesian (red-cone) species. In addition, we provide strong phylogenetic evidence for three distinct species (J. badia, J. conferta, J. lutchuensis) previously considered subspecies or varieties, as well as for the differentiation between the eastern and western Mediterranean lineages of J. macrocarpa. Our findings suggest that the Mediterranean basin was the primary center of diversification for Juniperus sect. Juniperus, followed by an East Asian-Tethyan disjunction resulting from uplifts of the Qinghai-Tibetan Plateau and climatic shifts. The colonization history of Macaronesia by red-cone junipers from the western Mediterranean appears to have taken place independently in two different geological periods: the Miocene (Azores) and the Pliocene (Madeira-Canary Islands). Overall, genomic data and phylogenetic analysis are key to consider a new taxonomic proposal and reconstruct the biogeographical history of the iconic needle-leaved junipers across the Paleartic.

Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae)

BACKGROUND AND AIMS

Polyploidy is considered one of the main mechanisms of plant evolution and speciation. In the Mediterranean Basin, polyploidy has contributed to making this region a biodiversity hotspot, along with its geological and climatic history and other ecological and biogeographical factors. The Mediterranean genus Centaurium (Gentianaceae) comprises ~25 species, of which 60 % are polyploids, including tetraploids and hexaploids. To date, the evolutionary history of centauries has been studied using Sanger sequencing phylogenies, which have been insufficient to fully understand the phylogenetic relationships in this lineage. The goal of this study is to gain a better understanding of the evolutionary history of Centaurium by exploring the mechanisms that have driven its diversification, specifically hybridization and polyploidy. We aim to identify the parentage of hybrid species, at the species or clade level, as well as assessing whether morphological traits are associated with particular ploidy levels.

METHODS

We sequenced RADseq markers from 42 samples of 28 Centaurium taxa, and performed phylogenomic analyses using maximum likelihood, summary coalescent SVDquartets and Neighbor-Net approaches. To identify hybrid taxa, we used PhyloNetworks and the fastSTRUCTURE algorithm. To infer the putative parental species of the allopolyploids, we employed genomic analyses (SNIPloid). The association between different traits and particular ploidy levels was explored with non-metric multidimensional scaling.

KEY RESULTS

Our phylogenetic analyses confirmed the long-suspected occurrence of recurrent hybridization. The allopolyploid origin of the tetraploid C. serpentinicola and the hexaploids C. mairei, C. malzacianum and C. centaurioides was also confirmed, unlike that of C. discolor. We inferred additional signatures of hybridization events within the genus and identified morphological traits differentially distributed in different ploidy levels.

CONCLUSIONS

This study highlights the important role that hybridization has played in the evolution of a Mediterranean genus such as Centaurium, leading to a polyploid complex, which facilitated its diversification and may exemplify that of other Mediterranean groups.

Challenge accepted: Evolutionary lineages versus taxonomic classification of North American shrub willows (Salix)

PREMISE

The huge diversity of Salix subgenus Chamaetia/Vetrix clade in North America and the lack of phylogenetic resolution within this clade has presented a difficult but fascinating challenge for taxonomists to resolve. Here we tested the existing taxonomic classification with molecular tools.

METHODS

In this study, 132 samples representing 46 species from 22 described sections of shrub willows from the United States and Canada were analyzed and combined with 67 samples from Eurasia. The ploidy levels of the samples were determined using flow cytometry and nQuire. Sequences were produced using a RAD sequencing approach and subsequently analyzed with ipyrad, then used for phylogenetic reconstructions (RAxML, SplitsTree), dating analyses (BEAST, SNAPPER), and character evolution analyses of 14 selected morphological traits (Mesquite).

RESULTS

The RAD sequencing approach allowed the production of a well-resolved phylogeny of shrub willows. The resulting tree showed an exclusively North American (NA) clade in sister position to a Eurasian clade, which included some North American endemics. The NA clade began to diversify in the Miocene. Polyploid species appeared in each observed clade. Character evolution analyses revealed that adaptive traits such as habit and adaxial nectaries evolved multiple times independently.

CONCLUSIONS

The diversity in shrub willows was shaped by an evolutionary radiation in North America. Most species were monophyletic, but the existing sectional classification could not be supported by molecular data. Nevertheless, monophyletic lineages share several morphological characters, which might be useful in the revision of the taxonomic classification of shrub willows.

Species delimitation 4.0: integrative taxonomy meets artificial intelligence

Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.

Chloroplast Genome Provides Insights into Molecular Evolution and Species Relationship of Fleabanes (Erigeron: Tribe Astereae, Asteraceae) in the Juan Fernández Islands, Chile

Erigeron represents the third largest genus on the Juan Fernández Islands, with six endemic species, five of which occur exclusively on the younger Alejandro Selkirk Island with one species on both islands. While its continental sister species is unknown, Erigeron on the Juan Fernández Islands appears to be monophyletic and most likely evolved from South American progenitor species. We characterized the complete chloroplast genomes of five Erigeron species, including accessions of E. fernandezia and one each from Alejandro Selkirk and Robinson Crusoe Islands, with the purposes of elucidating molecular evolution and phylogenetic relationships. We found highly conserved chloroplast genomes in size, gene order and contents, and further identified several mutation hotspot regions. In addition, we found two positively selected chloroplast genes (ccsA and ndhF) among species in the islands. The complete plastome sequences confirmed the monophyly of Erigeron in the islands and corroborated previous phylogenetic relationships among species. New findings in the current study include (1) two major lineages, E. turricola-E. luteoviridis and E. fernandezia-E. ingae-E. rupicola, (2) the non-monophyly of E. fernandezia occurring on the two islands, and (3) the non-monophyly of the alpine species E. ingae complex.

Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives

Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a "spectacular failure" due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here, we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed the polyphyly of others. Using an fbranch analysis, we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera.

Contrasting levels of β-diversity and underlying phylogenetic trends indicate different paths to chemical diversity in highland and lowland willow species

Diverse specialised metabolites contributed to the success of vascular plants in colonising most terrestrial habitats. Understanding how distinct aspects of chemical diversity arise through heterogeneous environmental pressures can help us understand the effects of abiotic and biotic stress on plant evolution and community assembly. We examined highland and lowland willow species within a phylogenetic framework to test for trends in their chemical α-diversity (richness) and β-diversity (variation among species sympatric in elevation). We show that differences in chemistry among willows growing at different elevations occur mainly through shifts in chemical β-diversity and due to convergence or divergence among species sharing their elevation level. We also detect contrasting phylogenetic trends in concentration and α-diversity of metabolites in highland and lowland willow species. The resulting elevational patterns contribute to the chemical diversity of willows and suggest that variable selective pressure across ecological gradients may, more generally, underpin complex changes in plant chemistry.

Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses

Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups. Both nuclear and plastome data recovered a well-resolved phylogeny. The species were divided into three main clades corresponding to their inflorescence types, - the racemose group, the solitary-flower group and the corymbose group - with the latter two sister to one another. Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago. The diversification of the three major clades began between the Paleocene and Miocene, suggesting that paleoclimatic events were an important driving force for Prunus diversification. Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences, and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis, respectively. We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies. Prunus has undergone extensive hybridization events, although it is difficult to identify conclusively specific instances of hybridization when using SNP data, especially deep in the phylogeny. Our study provides well-resolved nuclear and plastid phylogenies of Prunus, reveals substantial cytonuclear discord at shallow scales, and sheds new light on inflorescence evolution in this economically important lineage.

Meeting in Liguria: hybridisation between Apennine endemic Euphorbia barrelieri and western Mediterranean E. nicaeensis led to the allopolyploid origin of E. ligustica

The Mediterranean Basin is renowned for its extremely rich biota and is considered as one of the 25 Global Biodiversity Hotspots, but its diversity is not homogeneously distributed. Outstanding in the number of (endemic) species are the Ligurian Alps (Italy). At the foot of the Ligurian Alps, little above the Mediterranean Sea, a disjunct occurrence of Italian endemic Euphorbia barrelieri was reported. Using an array of integrative methods ranging from cytogenetic (chromosome number and relative genome size estimation), over phylogenetic approaches (plastid, ITS and RAD sequencing) to multivariate morphometrics we disentangled the origin of these populations that were shown to be tetraploid. We performed phylogenetic analyses of the nuclear ITS and plastid regions of a broad taxonomic sampling of Euphorbia sect. Pithyusa to identify possible species involved in the origin of the tetraploid populations and then applied various analyses of RADseq data to identify the putative parental species. Our results have shown that the Ligurian populations of E. barrelieri are of allotetraploid origin that involved E. barrelieri and western Mediterranean E. nicaeensis as parental species. We thus describe a new species, E. ligustica, and hypothesise that its adaptation to similar environments in which E. barrelieri occurs, triggered development of similar morphology, whereas its genetic composition appears to be closer to that of E. nicaeensis. Our study emphasises the importance of polyploidisation for plant diversification, highlights the value of the Ligurian Alps as a hotspot of biodiversity and endemism and underlines the importance of integrative taxonomic approaches in uncovering cryptic diversity.

Evolution of sex in crops: recurrent scrap and rebuild

Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.

Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex

Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with complex morphological patterns. In such TCGs, mosaic-like character combinations and conflicts of morphological data with molecular phylogenies present a major problem for species classification. Here, we used the large polyploid apomictic European Ranunculus auricomus complex to study relationships among five diploid sexual progenitor species and 75 polyploid apomictic derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal and stem leaves, receptacles), genomic data (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed genomic clusters correspond to morphological groupings based on basal leaves and concatenated traits, and morphological groups were best resolved with RAD-Seq data; (2) described apomictic taxa usually overlap within trait morphospace except for those taxa at the space edges; (3) apomictic phenotypes are highly influenced by parental subgenome composition and to a lesser extent by climatic factors; and (4) allopolyploid apomictic taxa, compared to their sexual progenitor, resemble a mosaic of ecological and morphological intermediate to transgressive biotypes. The joint evaluation of phylogenomic, phenotypic, reproductive, and ecological data supports a revision of purely descriptive, subjective traditional morphological classifications.

Insights into the Taxonomically Challenging Hexaploid Alpine Shrub Willows of Salix Sections Phylicifoliae and Nigricantes (Salicaceae)

The complex genomic composition of allopolyploid plants leads to morphologically diverse species. The traditional taxonomical treatment of the medium-sized, hexaploid shrub willows distributed in the Alps is difficult based on their variable morphological characters. In this study, RAD sequencing data, infrared-spectroscopy, and morphometric data are used to analyze the phylogenetic relationships of the hexaploid species of the sections Nigricantes and Phylicifoliae in a phylogenetic framework of 45 Eurasian Salix species. Both sections comprise local endemics as well as widespread species. Based on the molecular data, the described morphological species appeared as monophyletic lineages (except for S. phylicifolia s.str. and S. bicolor, which are intermingled). Both sections Phylicifoliae and Nigricantes are polyphyletic. Infrared-spectroscopy mostly confirmed the differentiation of hexaploid alpine species. The morphometric data confirmed the molecular results and supported the inclusion of S. bicolor into S. phylicifolia s.l., whereas the alpine endemic S. hegetschweileri is distinct and closely related to species of the section Nigricantes. The genomic structure and co-ancestry analyses of the hexaploid species revealed a geographical pattern for widespread S. myrsinifolia, separating the Scandinavian from the alpine populations. The newly described S. kaptarae is tetraploid and is grouped within S. cinerea. Our data reveal that both sections Phylicifoliae and Nigricantes need to be redefined.

Picks in the Fabric of a Polyploidy Complex: Integrative Species Delimitation in the Tetraploid Leucanthemum Mill. (Compositae, Anthemideae) Representatives

Based on the results of a preceding species-delimitation analysis for the diploid representatives of the genus Leucanthemum (Compositae, Anthemideae), the present study aims at the elaboration of a specific and subspecific taxonomic treatment of the tetraploid members of the genus. Following an integrative taxonomic approach, species-level decisions on eight predefined morphotaxon hypotheses were based on genetic/genealogical, morphological, ecological, and geographical differentiation patterns. ddRADseq fingerprinting and SNP-based clustering revealed genetic integrity for six of the eight morphotaxa, with no clear differentiation patterns observed between the widespread L. ircutianum subsp. ircutianum and the N Spanish (Cordillera Cantábrica) L. cantabricum and the S French L. delarbrei subsp. delabrei (northern Massif Central) and L. meridionale (western Massif Central). The inclusion of differentiation patterns in morphological (leaf dissection and shape), ecological (climatological and edaphic niches), and geographical respects (pair-wise tests of sympatry vs. allopatry) together with the application of a procedural protocol for species-rank decisions (the 'Wettstein tesseract') led to the proposal of an acknowledgement of the eight predefined morphotaxon hypotheses as six species (two of them with two subspecies). Nomenclatural consequences following from these results are drawn and lead to the following new combinations: Leucanthemum delarbrei subsp. meridionale (Legrand) Oberpr., T.Ott & Vogt, comb. nov. and Leucanthemum ruscinonense (Jeanb. & Timb.-Lagr.) Oberpr., T.Ott & Vogt, comb. et stat. nov.

Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section Suaveolentes (Solanaceae)

BACKGROUND AND AIMS

The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed <6 million years ago and radiated in the arid centre of Australia.

METHODS

We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework.

KEY RESULTS

RADseq generated a well-supported phylogenetic tree, in which multiple accessions from each species formed unique genetic clusters. Chromosome numbers and genome sizes vary from n = 2x = 15 to 24 and 2.7 to 5.8 pg/1C nucleus, respectively. Decreases in both genome size and chromosome number occur, although neither consistently nor in parallel. Species with the lowest chromosome numbers (n = 15-18) do not possess the smallest genome sizes and, although N. heterantha has retained the ancestral chromosome complement, n = 2x = 24, it nonetheless has the smallest genome size, even smaller than that of the modern representatives of ancestral diploids.

CONCLUSIONS

The results indicate that decreases in genome size and chromosome number occur in parallel down to a chromosome number threshold, n = 20, below which genome size increases, a phenomenon potentially explained by decreasing rates of recombination over fewer chromosomes. We hypothesize that, more generally in plants, major decreases in genome size post-polyploidization take place while chromosome numbers are still high because in these stages elimination of retrotransposons and other repetitive elements is more efficient. Once such major genome size change has been accomplished, then dysploid chromosome reductions take place to reorganize these smaller genomes, producing species with small genomes and low chromosome numbers such as those observed in many annual angiosperms, including Arabidopsis.

There and Back Again: The Unexpected Journeys of Metridium de Blainville, 1824 between the Old Oceans and throughout the Modern World

AbstractMembers of the sea anemone genus Metridium are abundant in temperate rocky habitats and fouling communities. Their biogeographic history is expected to reflect changes in currents and habitats that have influenced benthic communities, such as the climate-influenced changes that occurred during the Last Glacial Maximum. More recently, however, anthropogenic influences such as shipping transportation and the creation of artificial habitat have altered and affected the composition of modern-day marine communities. Here we use sequence-capture data to examine the genetic structure of Metridium across its shallow-water distribution to (1) evaluate species boundaries within Metridium, (2) elucidate the dispersal history of Metridium between and among oceans, and (3) assess the influence of anthropogenic movement on modern-day populations. We find strong evidence for two species within Metridium: M. farcimen and M. senile. Dispersal from the Pacific to the Atlantic included a subsequent isolation of a small population in or above the Bering Sea, which has presumably moved southward. Within the native range of M. senile, admixture is prevalent even between oceans as a result of anthropogenic activities. The nonnative populations in Chile and the Falkland Islands came from at least two distinct introduction events originating from both coasts of the United States in the North Pacific and North Atlantic Oceans. Hybridization between M. senile and M. farcimen is documented as occurring in anthropogenically influenced habitats. The heavy influence from anthropogenic activities will continue to impact our understanding of marine organisms, particularly within the native range and for those that are easily transported across long distances.

The Ovule Number Variation Provides New Insights into Taxa Delimitation in Willows (Salix subgen. Salix; Salicaceae)

Salix babylonica, S. alba and S. fragilis are closely related species characterized by the lanceolate, acuminate and serrulate leaves. The boundaries between them are defined by relatively few diagnostic characters, and their identification is not fully solved. Recent studies have demonstrated that the number of ovules present in the ovaries of the willow flower can assist in the identification of the species. The detailed ovule data, characteristic for flowers of each species, S. babylonica, S. alba and S. fragilis, and variation in the number of ovules per ovary were documented using many representatives of these species from various geographic regions. The data included the minimum and maximum number of ovules per valve and per ovary and the percentages of valves with a specific number of ovules in a catkin. Some intermediate genotypes and clusters with similar ovule indexes were observed. The important character for the identification of S. babylonica was the presence of valves with 1 or 2 ovules in the ovaries; S. fragilis had valves with 3 ovules while S. alba had the greater number (4-12).

Genomic evidence for contrasting patterns of host-associated genetic differentiation across shared host-plant species in leaf- and bud-galling sawflies

Resource specialization and ecological speciation arising through host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary timescales. We applied genome-wide single nucleotide polymorphism and mitochondrial DNA sequence data obtained through genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae) collected from seven shared willow (Salicaceae: Salix) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species compared with most bud gallers. In contrast to bud gallers, leaf gallers also exhibited statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and host shifts in two related galler groups that have radiated in parallel across a shared resource base indicate a lack of evolutionary repeatability in the focal system, and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.

Evolution of a hybrid zone of two willow species (Salix L.) in the European Alps analyzed by RAD-seq and morphometrics

Natural hybridization of plants can result in many outcomes with several evolutionary consequences, such as hybrid speciation and introgression. Natural hybrid zones can arise in mountain systems as a result of fluctuating climate during the exchange of glacial and interglacial periods, where species retract and expand their territories, resulting in secondary contacts. Willows are a large genus of woody plants with an immense capability of interspecific crossing. In this study, the sympatric area of two diploid sister species, S. foetida and S. waldsteiniana in the eastern European Alps, was investigated to study the genomic structure of populations within and outside their contact zone and to analyze congruence of morphological phenotypes with genetic data. Eleven populations of the two species were sampled across the Alps and examined using phylogenetic network and population genetic structure analyses of RAD Seq data and morphometric analyses of leaves. The results showed that a homoploid hybrid zone between the two species was established within their sympatric area. Patterns of genetic admixture in homoploid hybrids indicated introgression with asymmetric backcrossing to not only one of the parental species but also one hybrid population forming a separate lineage. The lack of F1 hybrids indicated a long-term persistence of the hybrid populations. Insignificant isolation by distance suggests that gene flow can act over large geographical scales. Morphometric characteristics of hybrids supported the molecular data and clearly separated populations of the parental species, but showed intermediacy in the hybrid zone populations with a bias toward S. waldsteiniana. The homoploid hybrid zone might have been established via secondary contact hybridization, and its establishment was fostered by the low genetic divergence of parental species and a lack of strong intrinsic crossing barriers. Incomplete ecological separation and the ability of long-distance dispersal of willows could have contributed to the spatial expansion of the hybrid zone.

Untying Gordian knots: unraveling reticulate polyploid plant evolution by genomic data using the large Ranunculus auricomus species complex

Speciation via hybridization and polyploidization is a major evolutionary force in plant evolution but is still poorly understood for neopolyploid groups. Challenges are attributed to high heterozygosity, low genetic divergence, and missing information on progenitors, ploidy, and reproduction. We study the large Eurasian Ranunculus auricomus species complex and use a comprehensive workflow integrating reduced-representation sequencing (RRS) genomic data to unravel reticulate evolution, genome diversity and composition of polyploids. We rely on 97 312 restriction site-associated DNA sequencing (RAD-Seq) loci, 576 targeted nuclear genes (48 phased), and 71 plastid regions derived from 78 polyploid apomictic taxa and four diploid and one tetraploid putative sexual progenitor species. We applied (phylo)genomic structure, network, and single nucleotide polymorphism (SNP)-origin analyses. Results consistently showed only 3-5 supported and geographically structured polyploid genetic groups, each containing extant sexual and one unknown progenitor species. Combined analyses demonstrated predominantly allopolyploid origins, each involving 2-3 different diploid sexual progenitor species. Young allotetraploids were characterized by subgenome dominance and nonhybrid SNPs, suggesting substantial post-origin but little lineage-specific evolution. The biodiversity of neopolyploid complexes can result from multiple hybrid origins involving different progenitors and substantial post-origin evolution (e.g. homoeologous exchanges, hybrid segregation, gene flow). Reduced-representation sequencing genomic data including multi-approach information is efficient to delimit shallow reticulate relationships.

From Western Asia to the Mediterranean Basin: Diversification of the Widespread Euphorbia nicaeensis Alliance (Euphorbiaceae)

The Mediterranean Basin is an important biodiversity hotspot and one of the richest areas in the world in terms of plant diversity. Its flora parallels in several aspects that of the Eurasian steppes and the adjacent Irano-Turanian floristic region. The Euphorbia nicaeensis alliance spans this immense area from the western Mediterranean to Central Asia. Using an array of complementary methods, ranging from phylogenomic and phylogenetic data through relative genome size (RGS) estimation to morphometry, we explored relationships and biogeographic connections among taxa of this group. We identified the main evolutionary lineages, which mostly correspond to described taxa. However, despite the use of highly resolving Restriction Site Associated DNA (RAD) sequencing data, relationships among the main lineages remain ambiguous. This is likely due to hybridisation, lineage sorting triggered by rapid range expansion, and polyploidisation. The phylogenomic data identified cryptic diversity in the Mediterranean, which is also correlated with RGS and, partly, also, morphological divergence, rendering the description of a new species necessary. Biogeographic analyses suggest that Western Asia is the source area for the colonisation of the Mediterranean by this plant group and highlight the important contribution of the Irano-Turanian region to the high diversity in the Mediterranean Basin. The diversification of the E. nicaeensis alliance in the Mediterranean was triggered by vicariance in isolated Pleistocene refugia, morphological adaptation to divergent ecological conditions, and, to a lesser extent, by polyploidisation.

Recurrent allopolyploidization, Y-chromosome introgression and the evolution of sexual systems in the plant genus Mercurialis

The plant genus Mercurialis includes dioecious, monoecious and androdioecious species (where males coexist with hermaphrodites). Its diversification involved reticulate evolution via hybridization and polyploidization. The Y chromosome of the diploid species Mercurialis annua shows only mild signs of degeneration. We used sequence variation at a Y-linked locus in several species and at multiple autosomal and pseudoautosomal loci to investigate the origin and evolution of the Y chromosome across the genus. Our study provides evidence for further cases of allopolyploid speciation. It also reveals that all lineages with separate sexes (with one possible exception) share the same ancestral Y chromosome. Surprisingly, males in androdioecious populations of hexaploid M. annua carry a Y chromosome that is not derived from either of its two putative progenitor lineages but from a more distantly related perennial dioecious lineage via introgression. These results throw new light on the evolution of sexual systems and polyploidy in Mercurialis and secure it as a promising model for further study of plant sex chromosomes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

Long-read genotyping with SLANG (Simple Long-read loci Assembly of Nanopore data for Genotyping)

PREMISE

Most phylogenomic library preparation methods and bioinformatic analysis tools in restriction site-associated DNA sequencing (RADseq)/genotyping-by-sequencing (GBS) studies are designed for use with Illumina data. The lack of alternative bioinformatic pipelines hinders the exploration of long-read multi-locus data from other sequencing platforms. The Simple Long-read loci Assembly of Nanopore data for Genotyping (SLANG) pipeline enables locus assembly, orthology estimation, and single-nucleotide polymorphism (SNP) calling using Nanopore-sequenced multi-locus data.

METHODS AND RESULTS

Two test libraries (Leucanthemum spp., Senecio spp.; Compositae) were prepared using an amplified fragment length polymorphism (AFLP)-based method to reduce genome complexity, then Nanopore-sequenced, and analyzed with SLANG. We identified 704 and 448 orthologous loci with 12,368 and 10,048 SNPs, respectively. The constructed phylogenetic networks were identical to a GBS network produced using Leucanthemum Illumina data and were consistent with Senecio species circumscriptions based on morphology.

CONCLUSIONS

SLANG identifies orthologous loci and extracts SNPs from long-read multi-locus Nanopore data for phylogenetic inference, population genetics, or phylogeographical studies. Combined with an AFLP-based library preparation, SLANG provides an easily scalable, cost-effective, and affordable alternative to Illumina-based RADseq/GBS procedures.

Towards accurate, contiguous and complete alignment-based polyploid phasing algorithms

Phasing, and in particular polyploid phasing, have been challenging problems held back by the limited read length of high-throughput short read sequencing methods which can't overcome the distance between heterozygous sites and labor high cost of alternative methods such as the physical separation of chromosomes for example. Recently developed single molecule long-read sequencing methods provide much longer reads which overcome this previous limitation. Here we review the alignment-based methods of polyploid phasing that rely on four main strategies: population inference methods, which leverage the genetic information of several individuals to phase a sample; objective function minimization methods, which minimize a function such as the Minimum Error Correction (MEC); graph partitioning methods, which represent the read data as a graph and split it into k haplotype subgraphs; cluster building methods, which iteratively grow clusters of similar reads into a final set of clusters that represent the haplotypes. We discuss the advantages and limitations of these methods and the metrics used to assess their performance, proposing that accuracy and contiguity are the most meaningful metrics. Finally, we propose the field of alignment-based polyploid phasing would greatly benefit from the use of a well-designed benchmarking dataset with appropriate evaluation metrics. We consider that there are still significant improvements which can be achieved to obtain more accurate and contiguous polyploid phasing results which reflect the complexity of polyploid genome architectures.

Molecular and morphological analyses clarify species delimitation in section Costatae and reveal Betula buggsii sp. nov. (sect. Costatae, Betulaceae) in China

BACKGROUND AND AIMS

Delineating closely related and morphologically similar species is difficult. Here, we integrate morphology, genetics, ploidy and geography to resolve species and subspecies boundaries in four trees of section Costatae (genus Betula): Betula ashburneri, B. costata, B. ermanii and B. utilis, as well as multiple subspecies and polyploid races.

METHODS

We genotyped 371 individuals (20-133 per species) from 51 populations at 15 microsatellite markers, as well as a subset of individuals, using restriction-site associated DNA sequencing and nuclear internal transcribed spacers. We determined the ploidy level of eight individuals using flow cytometry and characterized leaf variation for a subset of 109 individuals by morphometric analysis.

KEY RESULTS

Integration of multiple lines of evidence suggested a series of revisions to the taxonomy of section Costatae. Betula costata and B. ermanii were found to be valid. Molecular and leaf morphology analyses revealed little differentiation between diploid B. albosinensis and some samples of B. utilis ssp. utilis. By contrast, other B. utilis ssp. utilis samples and ssp. albosinensis formed a morphological continuum but differed based on genetics. Specifically, B. utilis ssp. albosinensis was divided into two groups with group I genetically similar to B. utilis ssp. utilis and group II, a distinct cluster, proposed as the new diploid species Betula buggsii sp. nov. Phylogenomic analysis based on 2285 620 single nucleotide polymorphisms identified a well-supported monophyletic clade of B. buggsii. Morphologically, B. buggsii is characterized by elongated lenticels and a distinct pattern of bark peeling and may be geographically restricted to the Qinling-Daba Mountains.

CONCLUSIONS

Our integrated approach identifies six taxa within section Costatae: B. ashburneri, B. buggsii, B. costata, B. utilis ssp. utilis, B. utilis ssp. albosinensis and B. ermanii. Our research demonstrates the value of an integrative approach using morphological, geographical, genetic and ploidy-level data for species delineation.

The phylogeny of Salix revealed by whole genome re-sequencing suggests different sex-determination systems in major groups of the genus

BACKGROUND AND AIMS

The largest genus of Salicaceae sensu lato, Salix, has been shown to consist of two main clades: clade Salix, in which species have XY sex-determination systems (SDSs) on chromosome 7, and clade Vetrix including species with ZW SDSs on chromosome 15. Here, we test the utility of whole genome re-sequencing (WGR) for phylogenomic reconstructions of willows to infer changes between different SDSs.

METHODS

We used more than 1 TB of WGR data from 70 Salix taxa to ascertain single nucleotide polymorphisms on the autosomes, the sex-linked regions (SLRs) and the chloroplast genomes, for phylogenetic and species tree analyses. To avoid bias, we chose reference genomes from both groups, Salix dunnii from clade Salix and S. purpurea from clade Vetrix.

KEY RESULTS

Two main largely congruent groups were recovered: the paraphyletic Salix grade and the Vetrix clade. The autosome dataset trees resolved four subclades (C1-C4) in Vetrix. C1 and C2 comprise species from the Hengduan Mountains and adjacent areas and from Eurasia, respectively. Section Longifoliae (C3) grouped within the Vetrix clade but fell into the Salix clade in trees based on the chloroplast dataset analysis. Salix triandra from Eurasia (C4) was revealed as sister to the remaining species of clade Vetrix. In Salix, the polyploid group C5 is paraphyletic to clade Vetrix and subclade C6 is consistent with Argus's subgenus Protitea. Chloroplast datasets separated both Vetrix and Salix as monophyletic, and yielded C5 embedded within Salix. Using only diploid species, both the SLR and autosomal datasets yielded trees with Vetrix and Salix as well-supported clades.

CONCLUSION

WGR data are useful for phylogenomic analyses of willows. The different SDSs may contribute to the isolation of the two major groups, but the reproductive barrier between them needs to be studied.

Little hope for the polyploid endemic Pyrenean Larkspur ( Delphinium montanum ): Evidences from population genomics and Ecological Niche Modeling

Species endemic to restricted geographical ranges represent a particular conservation issue, be it for their heritage interest. In a context of global change, this is particularly the case for plants which belong to high‐mountain ecosystems and, because of their ecological requirements, are doomed to survive or disappear on their “sky islands”. The Pyrenean Larkspur (Delphinium montanum, Ranunculaceae) is endemic to the Eastern part of the Pyrenees (France and Spain). It is now only observable at a dozen of localities and some populations show signs of decline, such as a recurrent lack of flowering. Implementing population genomics approach (e.g., RAD‐seq like) is particularly useful to understand genomic patterns of diversity and differentiation in order to provide recommendations in term of conservation. However, it remains challenging for species such as D. montanum that are autotetraploid with a large genome size (1C‐value >10 pg) as most methods currently available were developed for diploid species. A Bayesian framework able to call genotypes with uncertainty allowed us to assess genetic diversity and population structure in this system. Our results show evidence for inbreeding (mean G_IS = 0.361) within all the populations and substantial population structure (mean G_ST = 0.403) at the metapopulation level. In addition to a lack of connectivity between populations, spatial projections of Ecological Niche Modeling (ENM) analyses under different climatic scenarios predict a dramatic decrease of suitable habitat for D. montanum in the future. Based on these results, we discuss the relevance and feasibility of different conservation measures.

Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids

Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as "units". Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.

Peripheral structures in unlabelled trees and the accumulation of subgenomes in the evolution of polyploids

Many angiosperms have undergone some series of polyploidization events over the course of their evolutionary history. In these genomes, especially those resulting from multiple autopolyploidization, it may be relatively easy to recognize all the ξ sets of n homeologous chromosomes, but it is much harder, if not impossible, to partition these chromosomes into n subgenomes, each representing one distinct genomic component of ξ chromosomes making up the original polyploid. Thus, if we wish to infer the polyploidization history of the genome, we could make use of all the gene trees inferred from the genes in one set of homeologous chromosomes to construct a consensus tree, but there is no evident way of combining the trees from the ξ different sets, because we have no labelling of the chromosomes that is known to be consistent across these sets. We suggest here that lacking a consistent leaf-labelling, the topological structure of the trees may display sufficient resemblance so that a higher level consensus could be revealing of evolutionary history. This would be especially true of the peripheral structures of the tree, likely representing events that occurred more recently and have thus been less obscured by subsequent evolutionary processes. Here, we present a statistical test to assess whether the subgenomes in a polyploid genome could have been added one at a time. The null hypothesis is that the accumulation of chromosomes follows a stochastic process in which transition from one generation to the next is through randomly choosing an edge, and then subdividing this edge in order to link the new internal vertex to a new external vertex. We analyze the probability distributions of a number of peripheral tree substructures, namely leaf- or terminal-pairs, triples and quadruples, arising from this stochastic process, in terms of some exact recurrences. We propose some conjectures regarding the asymptotic behaviours of these distributions. Applying our analysis to a sugarcane genome, we demonstrate that it is unlikely that the accumulation of subgenomes has occurred one at a time.

Genetic diversity of Salixlapponum populations in Central Europe

Salixlapponum is a cold-tolerant relict species in Europe that occurs in several sites, probably reflecting previous migration routes of S.lapponum during the Pleistocene. However, only a few data are available on the genetic structures of populations of S.lapponum. In this study, we use PCR-ISSR markers to investigate genetic variation in 19 European populations of S.lapponum L. AMOVA analysis shows that most of the variation (55.8%) occurs within populations; variability among groups accounts for 19.7%. An AMOVA analysis based on four groups determined by STRUCTURE analysis shows similar results: variability of 54.1% within the population and variability of 18.9% between the four population groups, based on geographic regions. Within individual geographic groups, which are characterised by the studied populations, the lowest variability (as well as the highest homogeneity) was found in populations located in Belarus. The obtained results are consistent with our expectations that the European Lowland could be a significant geographic barrier for gene flow over large geographic distances for S.lapponum. Both the Scandinavian and Belarusian populations, as well as those coming from NE Poland, are characterised by significant genetic distinctiveness. However, some populations from NE Poland and the Sudetes show similarities with populations from other geographic regions, indicating existing genetic relationships between them. Moreover, the results suggest a fairly clear division of the population into 4 emerging geographic regions, although separated by a geographical barrier: the Polish lowland, which forms part of the larger geographic unit known as the European Lowland.

Highly Diverse Shrub Willows (Salix L.) Share Highly Similar Plastomes

Plastome phylogenomics is used in a broad range of studies where single markers do not bear enough information. Phylogenetic reconstruction in the genus Salix is difficult due to the lack of informative characters and reticulate evolution. Here, we use a genome skimming approach to reconstruct 41 complete plastomes of 32 Eurasian and North American Salix species representing different lineages, different ploidy levels, and separate geographic regions. We combined our plastomes with published data from Genbank to build a comprehensive phylogeny of 61 samples (50 species) using RAxML (Randomized Axelerated Maximum Likelihood). Additionally, haplotype networks for two observed subclades were calculated, and 72 genes were tested to be under selection. The results revealed a highly conserved structure of the observed plastomes. Within the genus, we observed a variation of 1.68%, most of which separated subg. Salix from the subgeneric Chamaetia/Vetrix clade. Our data generally confirm previous plastid phylogenies, however, within Chamaetia/Vetrix phylogenetic results represented neither taxonomical classifications nor geographical regions. Non-coding DNA regions were responsible for most of the observed variation within subclades and 5.6% of the analyzed genes showed signals of diversifying selection. A comparison of nuclear restriction site associated DNA (RAD) sequencing and plastome data on a subset of 10 species showed discrepancies in topology and resolution. We assume that a combination of (i) a very low mutation rate due to efficient mechanisms preventing mutagenesis, (ii) reticulate evolution, including ancient and ongoing hybridization, and (iii) homoplasy has shaped plastome evolution in willows.

Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the genus Rosa

Reticulation, caused by hybridization and allopolyploidization, is considered an important and frequent phenomenon in the evolution of numerous plant lineages. Although both processes represent important driving forces of evolution, they are mostly ignored in phylogenetic studies involving a large number of species. Indeed only a scattering of methods exists to recover a comprehensive reticulated evolutionary history for a broad taxon sampling. Among these methods, comparisons of topologies obtained from plastid markers with those from a few nuclear sequences are favored, even though they restrict in-depth studies of hybridization and polyploidization. The genus Rosa encompasses c. 150 species widely distributed throughout the northern hemisphere and represents a challenging taxonomic group in which hybridization and polyploidization are prominent. Our main objective was to develop a general framework that would take patterns of reticulation into account in the study of the phylogenetic relationships among Rosa species. Using amplicon sequencing we targeted allele variation in the nuclear genome as well as haploid sequences in the chloroplast genome. We successfully recovered robust plastid and nuclear phylogenies and performed in-depth tests for several scenarios of hybridization using a maximum pseudo-likelihood approach on taxon subsets. Our diploid-first approach followed by hybrid and polyploid grafting resolved most of the evolutionary relationships among Rosa subgenera, sections, and selected species. Based on these results, we provide new directions for a future revision of the infrageneric classification in Rosa. The stepwise strategy proposed here can be used to reconstruct the phylogenetic relationships of other challenging taxonomic groups with large numbers of hybrid and polyploid taxa.

Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb

Background and Aims: Quantifying genetic variation is fundamental to understand a species' demographic trajectory and its ability to adapt to future changes. In comparison with diploids, however, genetic variation and factors fostering genetic divergence remain poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies. Methods: We collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing. In addition, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high-quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations, complemented by genome size measurements and chromosomal counts. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables. Key Results: We found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modeling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria. Conclusion: Current findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.

Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights

PREMISE

Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb-Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times.

METHODS

Sampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off-target reads, and 10 fossils were used to calibrate dated trees.

RESULTS

Varying numbers of targeted loci and off-target plastomes were recovered from most taxa. Nuclear and plastid data confidently place Heptacodium with Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement of Zabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm-wide dating analyses, but many major splitting events date to the Eocene.

CONCLUSIONS

The Angiosperms353 probe set facilitated the assembly of a large, single-copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades.

nPhase: an accurate and contiguous phasing method for polyploids

While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy (https://github.com/OmarOakheart/nPhase). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids.

The Evolutionary History, Diversity, and Ecology of Willows (Salix L.) in the European Alps

The genus Salix (willows), with 33 species, represents the most diverse genus of woody plants in the European Alps. Many species dominate subalpine and alpine types of vegetation. Despite a long history of research on willows, the evolutionary and ecological factors for this species richness are poorly known. Here we will review recent progress in research on phylogenetic relationships, evolution, ecology, and speciation in alpine willows. Phylogenomic reconstructions suggest multiple colonization of the Alps, probably from the late Miocene onward, and reject hypotheses of a single radiation. Relatives occur in the Arctic and in temperate Eurasia. Most species are widespread in the European mountain systems or in the European lowlands. Within the Alps, species differ ecologically according to different elevational zones and habitat preferences. Homoploid hybridization is a frequent process in willows and happens mostly after climatic fluctuations and secondary contact. Breakdown of the ecological crossing barriers of species is followed by introgressive hybridization. Polyploidy is an important speciation mechanism, as 40% of species are polyploid, including the four endemic species of the Alps. Phylogenomic data suggest an allopolyploid origin for all taxa analyzed so far. Further studies are needed to specifically analyze biogeographical history, character evolution, and genome evolution of polyploids.

Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7

Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 scaffolds, and includes 31,501 predicted genes. Analyses of short-read sequence data that included female and male plants suggested a male heterogametic sex-determining factor on chromosome 7, implying that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii sex-linked region occupies about 3.21 Mb of chromosome 7 in females (representing its position in the X chromosome), probably within a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one-third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for further studies of sex-determining regions in the family Salicaceae, and sex chromosome evolution.

A phylogenomic approach resolves the backbone of Prunus (Rosaceae) and identifies signals of hybridization and allopolyploidy

The genus Prunus, which contains 250-400 species, has ample genomic resources for the economically important taxa in the group including cherries, peaches, and almonds. However, the backbone of Prunus, specifically the position of the racemose group relative to the solitary and corymbose groups, remains phylogenetically uncertain. Surprisingly, phylogenomic analyses to resolve relationships in the genus are lacking. Here, we assemble transcriptomes from 17 Prunus species representing four subgenera, and use existing transcriptome assemblies, to resolve key relationships in the genus using a phylogenomic approach. From the transcriptomes, we constructed 21-taxon datasets of putatively single-copy nuclear genes with 591 and 379 genes, depending on taxon-occupancy filtering. Plastome sequences were obtained or assembled for all species present in the nuclear data set. The backbone of Prunus was resolved consistently in the nuclear and chloroplast phylogenies, but we found substantial cytonuclear discord within subgenera. Our nuclear phylogeny recovered a monophyletic racemose group, contrasting with previous studies finding paraphyly that suggests repeated allopolyploidy early in the evolutionary history of the genus. However, we detected multiple species with histories consistent with hybridization and allopolyploidy, including a deep hybridization event involving subgenus Amygdalus and the Armeniaca clade in subgenus Prunus. Analyses of gene tree conflict revealed substantial discord at several nodes, including the crown node of the racemose group. Alternative gene tree topologies that conflicted with the species tree were consistent with a paraphyletic racemose group, highlighting the complex reticulated evolutionary history of this group.